Combining Applications and Webroot Directories

In the default setup of FMS 4.5, the video files for Flash streaming and the video files for HLS streaming sit in two separate directories.  Is there any reason why I should not adjust my config settings so both functions point to the same directory?  Essentially, I would like to make the "applications" directory and the "webroot" directory the same directory.  I would then only need to publish one MP4 file on my server.  Flash streaming and iOS streaming would both be using the same file.

Thanks.